The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition
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Journal of Fungi Review The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition Thomas Hartinger * and Qendrim Zebeli Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; [email protected] * Correspondence: [email protected] Abstract: The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials. Citation: Hartinger, T.; Zebeli, Q. Keywords: additive; anaerobic digestion; cattle; enzyme; anaerobic fungi; herbivore; Neocalli- The Present Role and New Potentials mastigomycota; rumen; silage of Anaerobic Fungi in Ruminant Nutrition. J. Fungi 2021, 7, 200. https://doi.org/10.3390/jof7030200 1. Introduction Academic Editor: Laurent Dufossé The metabolic processes in the rumen are of crucial importance in ruminant nutrition and decisively influence the host supply with energy and valuable nutrients. Hence, the Received: 23 February 2021 rumen microbiota is of key interest in this interdisciplinary research field. Although it is Accepted: 5 March 2021 Published: 10 March 2021 common consensus that the ruminal ecosystem comprises various distinct microbial groups, i.e., bacteria, protozoa, archaea, fungi, and viruses [1], the myriad of microbiota-related Publisher’s Note: MDPI stays neutral studies in ruminant nutrition, however, are predominantly focusing on bacteria. Whilst with regard to jurisdictional claims in also the domains archaea and protozoa gained attention in terms of methane emissions or published maps and institutional affil- intra-ruminal nitrogen (N) recycling [2,3], AF (phylum Neocallimastigomycota) have yet iations. been widely neglected in the wider ruminant nutrition research. However, these obligate anaerobes are commensals along the gastrointestinal tract of ruminants, being mainly present in the forestomach [4], and truly vital for sufficient fiber degradation by means of expressing various carbohydrate-active enzymes (CAZymes), which can be organized in cellulosomes, as well as physically penetrating plant material via rhizoidal systems [5–7]. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. In fact, AF and their capabilities are highly recognized among microbiologists and This article is an open access article comprehensive scientific efforts have been made regarding their taxonomy, lifecycle, and distributed under the terms and metabolic characterization, which recently was excellently summarized by Hess et al. [5]. conditions of the Creative Commons Notwithstanding, AF appear to be equally relevant to ruminant nutritionists, who continu- Attribution (CC BY) license (https:// ally seek for strategies to optimize ruminal fiber degradation, a process in which AF are creativecommons.org/licenses/by/ indeed substantially involved [5,7]. Likewise, this microbial clade seems significant for 4.0/). further aspects related to modern livestock feeding. Therefore, by portraying the current J. Fungi 2021, 7, 200. https://doi.org/10.3390/jof7030200 https://www.mdpi.com/journal/jof J. Fungi 2021, 7, 200 2 of 15 perception of AF in ruminant nutrition and outlining their potential in this research field, this review extends the perspective on AF and aims to stimulate scientific discourse on their relevance in modern ruminant feeding as well as sensitize ruminant scientists for these hidden champions in the gut. Since Hess et al. [5] provide an extensive status quo on AF live cycle and taxonomy, the present review will not cover those aspects, albeit a new fungal taxon has again been isolated in the meantime [8]. Similarly, the reader is further encouraged to consult the article of Vinzelj et al. [9] for general basics on AF as well as thorough considerations about their cultivation. 2. Current Perception of Anaerobic Fungi in Ruminant Nutrition In terms of microbiota-related research, the field of ruminant nutrition is doing tremen- dous efforts to understand how the gut microbiota can be shaped by feeding to optimize rumen fermentation, nutrient provision to the host, as well as gut health and ultimately prevent diseases along with improving animal performance. Thereby, major focus is placed on the rumen, i.e., the gut segment that harbors a highly complex microbial community enabling the energetic utilization of structural carbohydrates as well as providing key nutrients, such as protein and vitamins, to the host animal [1,10]. In the last decades, the hindgut microbiota also became a subject of increasing interest for ruminant nutritionists, particularly in relation to high-grain feeding and associated microbial dysbiosis [11]. With few exceptions and irrespective of gut segment investigated, bacteria represent the target domain in nutritional studies with ruminants, as exemplified by the survey of Hender- son et al. [12], who investigated the influence of diet on the ruminal microbiota composition on a global scale, exploring bacteria, archaea, and protozoa. Anaerobic fungi, however, have not been included in this specific study and although AF have been introduced as potent fiber degraders in relevant ruminant nutrition journals very early [7], these microorganisms remain mostly unconsidered so far [12–16]. Therefore, including AF in future ruminant nutrition studies should be the logical outcome, as otherwise, a holistic capture of the rumen microbiota and its implications on nutrition seem hardly feasible. As a complemental note, the authors like to direct additional awareness to AF in the hindgut, which may be more vital for equines at first sight. However, a considerable number of active AF is present in the ruminant’s lower gut [4,17] and since concentrate-rich feeding can shift substrate degradation from the rumen to the hindgut [18], it would be irrational to disregard the fungal population in this part of the gastrointestinal tract. Interestingly, the rumen simulation technique of Czerkawski and Breckenridge [19] constitutes an in vitro system suitable for long-term incubation that is widespread in rumi- nant nutrition and may be an excellent option for studying rumen AF in all its aspects. In fact, this system has already been used in the past to explore these microorganisms [20–22] and due to its continuous flow of the liquid fraction was actually deemed a better approach for investigating rumen AF than batch cultures [20]. 2.1. Ruminal Fiber Degradation It is well established that AF contribute significantly to ruminal fiber degradation by attacking plant cell walls in two ways, i.e., enzymatically, and physically [5–7]. Remarkably, recent research showed the affinity of fungal CAZymes for recalcitrant fiber [23], which may explain the particular significance of AF when feeding low-quality forage to ruminants. The authors, however, will not review explicitly on the enzymatic repertoire of AF as fungal CAZymes and the associated cellulosomes have been the subject of earlier reviews [5,24] and a current list of all fungal CAZymes discovered so far is provided by Hess et al. [5]. The synergistic activity of CAZymes, either individually or organized as cellulosomes, and mechanical penetration of plant cell wall by fungal hyphae results in an enhanced cleavage of fibrous structures by AF [5], which will also increase the access for other rumen cellulolytics and likely also proteolytics [2]. Indeed, cell wall degradation by AF can be higher than by bacteria under certain in vitro conditions [25,26] but quantifying the exact fungal contribution to fiber breakdown in the rumen is difficult. However, J. Fungi 2021, 7, 200 3 of 15 several in vitro and in vivo studies demonstrated the association between AF and an improved fiber degradability [25–28], which is also suggested by recent in vitro data from Ma et al. [26]. These authors investigated the impact of co-culturing methanogens with either AF or bacteria on in vitro degradation of rice and wheat straw, observing higher dry matter and fiber degradation in the presence of AF, the extent of which was similar to lignocellulose breakdown by whole ruminal content. Interestingly, acetate production was even higher in the co-occurrence of AF and methanogens than for whole ruminal content or methanogens and bacteria